Dear all,
We have made a small change to the YNiC cluster configuration.
Until now, each cluster job could use as much memory as they wanted.
This has been known to cause problems for users when they submit jobs
which require a large amount of RAM. If multiple jobs which require
large amounts of RAM are put onto the same machine, the jobs may run out
of memory. More problematically, it was sometimes the case that jobs
which did not require much RAM were the ones which failed.
To prevent this, we have added a default RAM limitation to the cluster.
Each "slot" is allocated 8G by default. If the job uses more than this,
it will be killed.
Jobs which require more RAM can still be run on the cluster. To do
this, you will simply need to tell the cluster how much memory to
reserve for your job - this will prevent your job from running out of
RAM by reserving enough for you. This can be done using the -l
h_vmem=xxG argument to the qsub command. We have documented this on the
wiki at:
https://www.ynic.york.ac.uk/docs/ITPages/IT/ClusterScripts
under the "Resource Limitations" section.
We estimate that this will not affect many users. For anybody who is
affected and are using qsub directly, the instructions above provide
information on how to request more RAM to be made available. If you are
find that you are getting memory allocation errors when using any of the
YNiC provided cluster commands (clusterFeat, clusterR, clusterMatlab,
clusterReconAll), or when using NAF, please contact
it-support(a)ynic.york.ac.uk and we will make sure that we adapt the
scripts to use the correct arguments with the qsub command.
If you have any questions, please contact it-support(a)ynic.york.ac.uk
Thanks,
Mark
--
Mark Hymers, Lecturer in Neuroimaging Methods
York NeuroImaging Centre and Department of Psychology
University of York, UK
Please note that my email address is: mark.hymers(a)ynic.york.ac.uk
Responses to messages sent to other addresses may be delayed
Hello All,
A gentle reminder that we mechanisms in place to allow you to provide MRI
images to those participants that request them. Please use this process
rather than printing out 'pictures' of brains.
Many thanks
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Many of you will be aware that we have recently experienced a few
hardware failures on the YNiC computing cluster. We have now escalated
these issues and the manufacturer has committed to attend on site to
attempt to resolve the existing issues. Without being too technical,
this process is essentially an overhaul of the current cluster and
requires two engineers.
Obviously, we are doing out utmost to get your cluster up and running
again but, considering the scale of the job, please be patient. We will
keep you updated.
Thanks,
--
André
************************************************************************
André Gouws
York Neuroimaging Centre
University of York
The Biocentre
York Science Park
Heslington
YO10 5NY
Tel: +44 (0) 1904 435327
Fax: +44 (0) 1904 435356
Dear All,
We have a system for providing CDs at YNiC. However, such is the number of
requests we have to deal with, we now need to rethink how to provide the
anatomical scan data to participants. What’s even more frustrating, is
that although we have a system that alerts participants that their CD is
ready, 58 remain uncollected. We are therefore being asked to allocate
considerable resource to generating CDs that the participants subsequently
have little or no interest in.
Rethink: Moving forward, we will allow researchers to create data CDs for
their participants. The researcher will need to provide their own CD and
execute a script. The script, 'Create subject CD', can be run from the
'Applications' menu under 'YNiC Utilities'. Please follow the instructions
given by the script and note that you (1) have to have the permission of
the participant (2) make sure that the participant receives the CD [you may
want to record their signature] and (3) you record who you have sent CDs to.
Andre is also putting a webpage together to give guidance.
https://www.ynic.york.ac.uk/information/mri/MakeASubjectCD
Requests to YNiC for data CDs will no longer be met after 1/11/2016.
Thank you
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear Users,
Today we will be graced with the presence of Dr Helen Nutall from the
Psychology Department at Lancaster University. She will be giving a talk
entitled:
"Sensorimotor processing in perception of degraded speech"
The talk will be held in room B020 in the Psycholgy Department, at 4pm.
All are welcome and refreshments will be served afterwards.
Best,
Junior
--
Junior Whiteley
York Neuroimaging Centre
junior.whiteley(a)ynic.york.ac.uk
Hello All,
It has been noted that investigators are sometimes asking potential
participants screening questions in reception and other areas where
confidential answers may be overheard. Please make appropriate
arrangements to ensure the confidentiality of your participants responses.
Many thanks
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello everyone,
To avoid confusion for those recently joining the ynic user community,
Thursday seminars are announced, usually early in the week. This week there
is no seminar.
Best wishes
Tony
Hi all,
At the following times during this term, YNiC open plan will be closed
for teaching.
Please note that if any YNiC open plan computers have been left logged
on at the start of the teaching sessions, they will be automatically
logged out.
Week 2:
* Tuesday 4th October 1200-1600
* Thursday 6th October 0900-1300
Week 3:
* Monday 10th October 1200-1600
Week 4:
* Monday 17th October: 1200-1600
Week 7:
* Monday 7th November: 1200-1600
Week 9:
* Monday 21st November: 1200-1600
Timings for the Spring term will be sent around in December.
Thanks,
Mark
--
Mark Hymers, Lecturer in Neuroimaging Methods
York NeuroImaging Centre and Department of Psychology
University of York, UK
Please note that my email address is: mark.hymers(a)ynic.york.ac.uk
Responses to messages sent to other addresses may be delayed
Dear All,
Many of the routine updates to our IT provision have been successfully
completed. We will complete the remaining jobs next week. These involve
the stimulus PCs.
The cluster is currently down. This is an issue that is unrelated to the
routine updates and is being dealt with by HP engineers.
Thanks, Paul, for installing these important updates.
As I wrote previously, please report any issues that arise in your use of
the IT system here (other than the cluster issue, which we know about).
This will help us resolve them speedily.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear All,
A few things to update you on that will be occurring at YNiC over the next
couple of weeks.
During the weeks commencing 5th September and 12th September we will be
performing essential IT maintenance. This is the normal annual procedure
to install updates (as specified below). It will impact on access to the
centre and its IT provision as follows.
1) We will be closing the centre from 5pm, Monday 6th September through to
9am, Wednesday 7th September. There will be no access to computing during
this period.
2) For the week commencing 12th September we will have a ‘soft’ closure.
You may come to the centre, but your work may be disrupted by maintenance
of hardware and software. It may also be a period during which we have to
close the centre at short notice.
We should be able to honour scanner bookings during the fortnight, but
again there may be instances when we have to cancel them at short notice.
OVERVIEW OF UPDATES:
We will be updating our desktop and stimulus PC images. This will mean
that software versions will change. We make every effort to check that
these have minimal impact on researchers’ ability to run their analysis and
stimulus code. However, once our updates are made please check your use of
software to ensure it still works.
Thank you for your patience
Tony
--
Antony Morland, PhD
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
